3VP6 | pdb_00003vp6

Structural characterization of Glutamic Acid Decarboxylase; insights into the mechanism of autoinactivation

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	PLP-dependent transferases	8101725	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8101725	3000954	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Chorismate_bind	e3vp6B2	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Chorismate_bind	ECOD (develop294)
A	Chorismate_bind	e3vp6A2	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Chorismate_bind	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.90.1150.170	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1		CATH (4.3.0)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
A	3.90.1150.170	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1		CATH (4.3.0)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00282	Pyridoxal-dependent decarboxylase conserved domain (Pyridoxal_deC)	Pyridoxal-dependent decarboxylase conserved domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Glutamate decarboxylase 1	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding glutamate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity identical protein binding vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding glutamate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity identical protein binding protein binding	gamma-aminobutyric acid metabolic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process non-proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process gamma-aminobutyric acid biosynthetic process small molecule metabolic process gamma-aminobutyric acid metabolic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process non-proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process gamma-aminobutyric acid biosynthetic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process non-proteinogenic amino acid biosynthetic process trans-synaptic signaling synaptic signaling regulation of biological process signaling anterograde trans-synaptic signaling biological regulation cell-cell signaling chemical synaptic transmission cell communication behavior multicellular organismal process biological process involved in intraspecies interaction between organisms social behavior catabolic process organic acid catabolic process dicarboxylic acid catabolic process alpha-amino acid metabolic process succinate metabolic process carboxylic acid catabolic process gamma-aminobutyrate shunt glutamate metabolic process amino acid catabolic process L-glutamate catabolic process dicarboxylic acid metabolic process L-amino acid catabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process small molecule catabolic process locomotory behavior exploration behavior locomotory exploration behavior	presynapse cellular anatomical structure synapse cell junction presynaptic active zone cell periphery cell cortex intracellular anatomical structure cytoplasm perinuclear region of cytoplasm plasma membrane membrane membrane-bounded organelle vesicle membrane presynapse cellular anatomical structure synapse cell junction presynaptic active zone cell periphery cell cortex intracellular anatomical structure cytoplasm perinuclear region of cytoplasm plasma membrane membrane membrane-bounded organelle vesicle membrane organelle vesicle organelle membrane axon neuron projection axon terminus plasma membrane bounded cell projection cell projection distal axon neuron projection terminus clathrin-sculpted gamma-aminobutyric acid transport vesicle clathrin-sculpted vesicle intracellular vesicle clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane intracellular membrane-bounded organelle intracellular organelle coated vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle clathrin-coated vesicle coated vesicle clathrin-coated vesicle membrane GABA-ergic synapse inhibitory synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B	IPR002129	Pyridoxal phosphate-dependent decarboxylase, major domain	Domain
A, B	IPR021115	Pyridoxal-phosphate binding site	Binding Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q99259	cerebral palsy, spastic quadriplegic, 1 schizophrenia acquired hyperprolactinemia cocaine abuse epilepsy major depressive disorder bipolar disorder cocaine dependence glioblastoma Involutional Depression lung cancer malignant ependymoma Alzheimer disease autism opiate dependence cerebral palsy, spastic quadriplegic, 1 schizophrenia acquired hyperprolactinemia cocaine abuse epilepsy major depressive disorder bipolar disorder cocaine dependence glioblastoma Involutional Depression lung cancer malignant ependymoma Alzheimer disease autism opiate dependence peripheral nervous system disease pilocytic astrocytoma Down syndrome spastic quadriplegia hyperprolactinemia lung carcinoma malignant glioma adrenal cortex carcinoma medulloblastoma astrocytic tumor nasopharyngeal carcinoma pancreatic intraductal papillary-mucinous carcinoma peripheral neuropathy primitive neuroectodermal tumor Sjogren syndrome drug-induced dyskinesia intellectual disability large cell medulloblastoma atypical teratoid rhabdoid tumor oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm Pick disease depressive disorder

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	LLP	Parent Component: LYS RESID: AA0119 PSI-MOD : N6-pyridoxal phosphate-L-lysine MOD:00128

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.